Reality Shattered
by SGAFan
Summary: Spoilers for Progeny and The Real World SGA 3x05 and 3x06What happened to Elizabeth and how did she get to the infirmary as we saw her in The Real World? Who found her, and how?


_**Reality Shattered**_

_Missing scene between Progeny and The Real World_

_**Prologue:**_

Blackness filled her vision, chasing away the light despite her best efforts to hang onto it. Her grip on the railing weakened and her knees buckled. She tried to reach for her radio, but her efforts were futile as her leaden arm refused to obey. The cold floor rushed up to greet her and panic coursed through her body, as her tedious grip on consciousness slipped away. "Help…" she whispered.

But, as her last flicker of awareness was extinguished, Elizabeth knew no one was there to hear her plea.

Tension hastened John's stride. A small part of him wondered at it, even as his quick steps carried him up the stairs to the control room. Realistically, there wasn't a good reason why he felt like something was wrong, but, his intuition… his gut told him otherwise and John had learned long ago to listen to it.

At the top of the control room stairs, he paused and stared at Elizabeth's empty office. His gaze narrowed. He never expected to find her there, but he would've loved to been proven wrong.

John crossed the control room and headed directly towards Zelenka, who was working quietly at ops. "Radek? Have you seen Elizabeth?" He waited semi-patiently as Zelenka looked up and blinked. John knew the look well; he'd seen it many times when he'd interrupted Zelenka's concentration. Unlike Rodney, who spouted some snide remark, Zelenka always took a quiet moment to switch gears and focus on what was being asked of him.

"What? No. Not for the last hour or so." he looked around, his gaze passing over her office. "Did you try her on the radio?"

John sighed. "More than once. No answer."

Zelenka thought for a moment. "She did look tired. Maybe she went to quarters to get some rest?"

John looked away. "Already tried that," he muttered, "she wasn't there…"

_John knocked insistently on the door. "Elizabeth? It's John." Impatiently, he sighed loudly as only silence greeted his hail. He knocked again, this time louder. "Elizabeth?" John grimaced as he stared at the door. Something wasn't right. He couldn't place his finger on what, but he knew something was wrong. His eyes settled on the door crystal. As military commander, he could override anyone's security code at any time, but he knew a faster way to gain entrance. The Ancient gene he carried had a lot of benefits, not the least of which was being able to open almost any door he wanted, whenever he wanted. John rarely used that skill; he respected people's privacy too much, but this time his sense of urgency overrode it. _

_He reached out placing his hand gently over the door controls. "Open," he muttered. Atlantis obliged, and John quickly strode into Elizabeth's quarters. He did a quick search before stopping in the center and grimacing at the emptiness…_

John looked back at Zelenka. "Put me on citywide," he ordered.

Zelenka tapped a control on the Ancient console. "Channel open."

"Dr. Weir, this is Sheppard, please respond." John looked up almost as if he expected her voice to float into his sight. "Dr. Weir, this is Colonel Sheppard, please respond," he repeated. Another moment of silence passed before he looked at Zelenka and nodded for the doctor to close the channel. He stared hard into the doctor's eyes. "Something's not right, Radek." He held Zelenka's gaze for a moment, before the doctor nodded slowly.

"Let me calibrate internal sensors and see if we can locate her. She must be alone, otherwise she would've responded, or…" Zelenka glanced at John, "someone with her would have," he finished quietly.

John ground his teeth and nodded curtly. The implication of Zelenka's words wasn't lost on him. If she were unable to respond, someone would've said something. _Unless she's alone and not able to answer…_ "Find her." John's voice was curt as he reached up and tapped his headset. "McKay, this is Sheppard. Report to the control room immediately."

"This is McKay," Rodney's annoyed voice answered, "can it wait? I'm busy at the moment."

"No, it can't. Now, Rodney," John ordered.

"On my way," Rodney replied, all annoyance gone from his voice.

John looked back at Zelenka. "Anything?" His gaze switched to the biometric display. Life sign signals showed all over the central tower and beyond as the entire population of Atlantis was represented. He sighed loudly. "Which one is she?"

"Every human life sign in Atlantis registers with the biometric sensors…" Zelenka's voice trailed off.

John tore his gaze from the display and stared at the stoic expression on Zelenka's face. Cold realization hit him. "Do a head count. Make sure that the number of life signs we're reading matches the number of personnel we have on Atlantis," he ordered.

"What's going on?"

Rodney's voice distracted John. He turned. "Something's wrong. Elizabeth's not answering her radio or a citywide hail. She's not in the mess or her quarters either."

"You did a citywide hail? Rodney grimaced in confusion.

"Loud opera again, Rodney?" Zelenka piped in.

"I was thinking!" Rodney snapped. "There something about opera…"

"The _point_ is," John interrupted firmly, squashing the coming debate before it even started, "Elizabeth is missing. Radek is doing a comparison between Atlantis' personnel count and the life signs we're registering right now."

Rodney paled. "You're not suggesting…"

"I'd prefer to look at it as eliminating the possibility." John stared solemnly at Rodney.

"Right." Rodney stepped around Zelenka, sat down, and pulled one of the laptops to him. He started furiously tapping the keyboard.

Zelenka looked at Rodney's computer for a moment. "I am running comparison now, Rodney," he said patiently.

"Yes, yes!" Rodney took a moment to wave a hand in Zelenka's general direction. "But, using your methods we'll be at this all day!"

Zelenka glared at him for a moment, before muttering in Czech and looking away.

Oblivious to Zelenka, Rodney's hands flew over the keyboard. "Done," he hit the enter key triumphantly and scooted back from the computer. All triumph left his face as he stared at the figures. "Oh God…"

John looked over his shoulder and a cold cramp constricted his gut. "We're short one person," his voice was quietly solemn. He turned away for a moment, his gaze finding the inactive Stargate. _Elizabeth…_

"Maybe it's not her that's missing," Rodney's voice was slightly panicked. "I mean it could be someone else, we don't know for sure…"

John clenched his jaw and pulled in a deep breath before turning back and staring grimly at Rodney.

"Yeah," Rodney's voice was quiet, "I'm not buying that either."

"Put me on citywide," John ordered.

Rodney spun in his chair and tapped the intercom. "You're on, Colonel."

"Attention all personnel," John added a note of authority to his voice. "This is Colonel Sheppard. We have a situation on Atlantis. All civilian personnel are ordered to stay where they are until instructed otherwise. All military personnel, report to the Gate Room. Sheppard out." John stared at the schematic of the city for a moment, fighting the frustration and dread in him. They'd explored about half the city and Elizabeth could be anywhere in that half or beyond. "Is there _any _way at all to locate her?" John couldn't keep the note of frustration from his voice. When Rodney didn't answer, John turned and looked at his pale face. "Rodney?" He prompted again.

Rodney blinked hard. "Right." He turned and started tapping commands on the laptop again. "I could recalibrate the sensors to pick up any human…" his voice trailed off as he paused in his typing for a moment. "Well, anything, human in origin," he finished quietly before starting to type again.

"Do whatever you have to." John answered.

"Sir?" Major Lorne walked into the control room.

John faced him. "Major," he nodded once, curtly. "Dr. Weir is missing and not showing on the biometric sensors."

Lorne's eyes widened. "Colonel, you're not saying…"

"We don't know anything for sure, Major," John cut Lorne off. "Organize the men into search teams and prepare for a level to level search."

"Yes, sir," Lorne responded before he turned and walked briskly towards the stairs.

"Huh," Rodney grunted, "that's weird."

John walked to Rodney and looked over his shoulder. "What's weird?"

Rodney pointed at a yellow flashing dot in the east pier. "That. It's a life sign… sort of… well, maybe…"

John's gaze fixed on the dot. "Is it, or isn't it?" he snapped. "And what does the yellow coloring mean?"

"I don't know," Rodney shook his head. "It's almost like Atlantis' sensors can't decide what it is, so its not being labeled as anything the sensors recognize. Blue for human, red for Wraith, etcetera. It's like it's a… pseudo life form… or something…"

"Pseudo life-form," John muttered, "I don't like the sound of that. Elizabeth's missing, we're getting weird readings on the biometric sensors… that's too much of a coincidence for me." He straightened and tapped Rodney on the shoulder. "Grab a Life Signs Detector," he ordered. "You're with me. Let's check it out." John looked at Zelenka. "Keep tabs on it in real time, and let me know if anything changes. Keep trying to figure out what…" he waved aimlessly at the display, "it is." He turned and headed for the stairs, Rodney right behind him.

John descended the stairs and walked up to Lorne, Teyla and Ronon. "We've picked up an unknown reading in the east pier. The city's biometric sensors can't identify it. Major, bring your team. We need to check it out." John waved at one of the Marines standing nearby. "Give me your vest and P-90." He gestured at another solider. "Give McKay your tac vest and sidearm." John shrugged into his tac vest a checked the load on the P-90, as Rodney strapped a nine mil holster around his thigh. John's eyes passed over his team before he nodded once at Lorne. "Let's move out."

Using the transporter, it didn't take them long to reach the edge of the east pier. John raised his gun and paused outside the door where the anomalous reading had been registering. He glanced at Rodney. "Anything?"

"If you mean 'is it still there' yes. If you mean 'anything new' no," Rodney snapped.

His patience stretched to the breaking point, John glared at Rodney. "McKay," he answered through clenched teeth.

Rodney nodded once and fell silent as he touched a few keys on the LSD. "Nothing's different, that I can tell." Rodney tapped his radio. "Radek, this is Rodney. Any changes?"

"No," Zelenka answered, "nothing. I cannot find calibration on sensors to identify what it is."

"That's entirely _not_ helpful," Rodney muttered, "McKay out."

John stared at the door. "Great," he sighed. He glanced at Rodney. "McKay." John motioned with his head for Rodney to step clear of the door. "Teyla, Ronon." John stood in the dead center of the doorway, as Teyla and Ronon came up and stood shoulder to shoulder with him. He flipped the safety off on his P-90 and glanced pointedly at Teyla. John stared intently at the doors as Teyla passed her hand over the controls and the doors parted.

Nothing could've prepared John for what met his eyes.

Over the top of his P-90, John's gaze focused on the slight, prone form lying motionless on the far side of the large, exterior balcony.

"Oh my God…" Rodney muttered.

The moment of shock fled John. "Elizabeth!" John shouted. "Lorne! Watch our six!" He lowered his gun and broke into a fast run, Teyla, Ronon and Rodney right behind him. Dread, combined with urgency fueled his lengthening stride. _No… damn it!_

"Wait!" Rodney shouted, "Stop! Don't touch her!"

Barely ten feet from her body, John staggered to a stop. "What?" He snapped before taking another step towards Elizabeth. "McKay?" he insisted through clenched teeth. _Move, Elizabeth… be alive! _"Rodney!" he barked as he looked back.

"Don't touch her!" Shock blanketed Rodney's face as he looked up and met John's gaze. "She's infected with nanites. You touch her, you'll be infected as well."

John looked back at her prone form, as he took a reflexive step back. "Nanites…" he shook his head. "Can you tell if she's alive or not?"

An exasperated sigh preceded Rodney's response. "No. This thing just isn't sensitive enough. I can't tell if the readings are the nanites, or her."

"Damn it," John hissed. He turned his head. "Lorne! Get Beckett and a team in hazmat suits down here, now!" He glanced at Rodney who activated his radio.

"Radek, Dr. Weir is infected with nanites. Find a way to calibrate the biometric sensors to accommodate for that and figure out if she's alive or not."

"I will do my best," Zelenka responded.

"Well, do it fast!" Rodney snapped.

John licked his lips and tried to quell the frustration within him, as he stood helpless and stared at Elizabeth's still body. His gaze narrowed as he searched vainly for some sign of life; movement, breathing… anything. After everything they'd gone through together, everything they'd survived, John refused to believe it was over; that she was…

He shook his head and turned away from that one thought. _No!_ "Come on, Elizabeth," he muttered, "hang in there…"

"I don't see her breathing," Ronon commented quietly.

John's nod was barely discernable. "I know," he whispered. Letting his gun hang from his tac vest, John slowly walked towards her. The helplessness was more than he could tolerate and he was done waiting.

"Colonel?" Teyla questioned.

"What are you doing?" Rodney's voice found John, "did I _not _just say don't touch her?"

John took a moment to shoot a cold glare at Rodney. "I know," he growled. Barely a foot away from her, John slowly knelt. He stared at her pale and drawn faced for a moment before slowly reaching towards her.

"Sheppard." Ronon's voice was warning as he took a step towards John.

"I'm not going to touch her!" John spat. His knuckles scarcely an inch from her nose, John held his hand still and waited, the tense anticipation stealing his breath. "Come on," he whispered. After a long moment, John sighed deeply as her warm breath flowed over his hand. He allowed a slight smile as he looked up at his team members. "She's alive." On the heels of his statement, Zelenka's voice came over the radio.

"I have calibrated sensors to account for nanites. Dr. Weir is alive, but the nanite infestation in her body is extensive."

John's smile faded as he pulled back his hand, rested it on his bent knee and stared down at her. Somehow, he wasn't surprised. Relieved, yes, but not surprised. From the moment, two years ago, when she'd stared him in the eye and told him to shut up and listen to her, John had seen a formidable strength within Elizabeth Weir; far more then he would've ever give her credit for had they not lived through all that they had since arriving in Pegasus. For the past two years, he'd only seen that strength and resolve grow, and with it, his admiration and respect for her.

The sound of Beckett's approaching team snapped him from his thoughts and he slowly stood, backing out of their way.

Beckett paused for a moment and eyed John. "Did ye touch her, Colonel?"

John shook his head. "No. Rodney warned us off."

Beckett nodded silently and knelt by Elizabeth.

John stared at her as Beckett's team began assessing her condition. He set his mouth in a hard line. She'd survive. Atlantis and everyone here needed her… and because of that, she'd live. John's gaze narrowed in blunt determination. He'd make sure of it.

Author's notes: Well, this was supposed to be a drabble… LOL From the first time I watched The Real World, I wondered who and how they'd found her when the nanite infection had set in. *G* 


End file.
